Abstract
Spatial omics technologies generate wealthy but highly complex datasets. Here we present Spatial Omics DataBase (SODB), a web-based platform providing both rich data resources and a suite of interactive data analytical modules. SODB currently maintains >2,400 experiments from >25 spatial omics technologies, which are freely accessible as a unified data format compatible with various computational packages. SODB also provides multiple interactive data analytical modules, especially a unique module, Spatial Omics View (SOView). We conduct comprehensive statistical analyses and illustrate the utility of both basic and advanced analytical modules using multiple spatial omics datasets. We demonstrate SOView utility with brain spatial transcriptomics data and recover known anatomical structures. We further delineate functional tissue domains with associated marker genes that were obscured when analyzed using previous methods. We finally show how SODB may efficiently facilitate computational method development. The SODB website is https://gene.ai.tencent.com/SpatialOmics/. The command-line package is available at https://pysodb.readthedocs.io/en/latest/.
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Data availability
All the primary links of raw data are provided on the web page of datasets. All processed data can be downloaded via the SODB website (https://gene.ai.tencent.com/SpatialOmics/) or pysodb package (https://pysodb.readthedocs.io/en/latest/).
Code availability
The SODB website is available at https://gene.ai.tencent.com/SpatialOmics/. Code for the SODB project is available at https://github.com/yuanzhiyuan/SODB_analysis/. Code for pysodb is available at https://github.com/TencentAILabHealthcare/pysodb. Please refer to Supplementary Table 9 for detailed information on code and resources.
Change history
17 March 2023
A Correction to this paper has been published: https://doi.org/10.1038/s41592-023-01844-9
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Acknowledgements
Z.Y. acknowledges the support from the Shanghai Municipal Science and Technology Major Project (no. 2018SHZDZX01), ZJ Laboratory, Shanghai Center for Brain Science and Brain-Inspired Technology and 111 Project (no. B18015). M.Q.Z. acknowledges support by the Cecil H. and Ida Green Distinguished Chair. We thank L. Wang of Tencent for technical support.
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Contributions
J.Y., Z.Y. and M.Q.Z. designed the project. Z.Y. performed data collection. Website design was by Z.Y. and X.Z. J.Y., X.L. and Y.Z. provided technical support. Biological interpretation was by M.Q.Z. and Y.Z. Data statistics were performed by Z.Y. Website implementation was by X.Z. and W.P. Figure generation was by Z.Y. and F.Z. Z.Y. and W.P. wrote the manuscript. Z.X. maintains the website. J.Y. and M.Q.Z. reviewed the manuscript. All authors approved the final manuscript.
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Supplementary Figs. 1–42, Notes 1 and 2 and Tables 7–10.
Supplementary Table 1
Experiment information of SODB.
Supplementary Table 2
Dataset information of SODB.
Supplementary Table 3
Biotechnology information of SODB.
Supplementary Table 4
Review article containing computational methods.
Supplementary Table 5
Computational methods and their categories.
Supplementary Table 6
Datasets of SODB used by computational methods.
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Yuan, Z., Pan, W., Zhao, X. et al. SODB facilitates comprehensive exploration of spatial omics data. Nat Methods 20, 387–399 (2023). https://doi.org/10.1038/s41592-023-01773-7
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DOI: https://doi.org/10.1038/s41592-023-01773-7
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